I didn't have a problem with the cops taking back the city. There was still a payoff there. It was full circle, we start with a corrupt police force in BB and TDK, but by the end of TDKR they are defending Gotham alongside the Batman. Cops are people too. Who were the biggest heroes on 9/11? Cops and firefighters who inspired an entire country.

TDK showed that Batman didn't want civilians literally physically fighting when they're not qualified for it. "That wasn't exactly what I had in mind when I said I wanted to inspire people". Now, I wouldn't have had a problem with some tougher civilians entering the battle, but I think from a visual standpoint it helped reinforce the war theme better to have all the police in their uniforms vs. the mercenaries in their wardrobe.